Giovanni is a much more classic villain archetype and the fact that his true motives are still a mystery make him all the more mysterious. You know his organization is stealing pokemon and selling them, but that's all...he's just a crime lord at first glance, but you just know that there's something deeper to it...
Or he's just the classic mob boss/Bondian villain, which actually still makes him even more bad ass and generally awesome (in my opinion, at least) than the other villains in the main games. I mean, the villains of the main games in a nutshell:
Cyrus: "I want to capture the legendaries of time and space and dimensions in order to reshape the universe to my liking. Because I think I'm God or something like that."
Maxie: "I want to control Groudon to expand the land because I have a really perverted sense of what's good for everyone."
Archie: "I want to control Kyogre to expand the seas because I have a really... perverted... Hey, wait a second!"
Giovanni: "I want to take over the world. Because I have nothing better to do."
In other words, sure, the villains of the newer games are creepy, twisted, and have actual defined motivations, but their motivations tend to either be cliché (Sorry, Cyrus, but you've just described the desires of about 90% of all anime villains right there.) or those of good guys at heart. (It's my firm belief that Teams Aqua and Magma are just like PETA. You know they're doing things with good intentions in mind, but they're really,
really doing it wrong sometimes.)
In the meantime, Giovanni's just the kind of person who would order people to create a biological superweapon and giant mechanical robots of destruction with the intent to take over the world not because he wants to reshape it or anything but instead because it's just there, so why not?
If he does have something deeper underlying his motivations, it probably has something to do with strapping a secret agent to a metal slab and holding the world for ransom with a doomsday device. ...Which would also be because he could, not because he really particularly needed the money.
But the point is to this entire tl;dr post, I totally agree with the comments that Giovanni is a classic villain and that that's what makes him seriously awesome.